"Skynet IS the virus", Of course Brewster knew that Skynet was operational, it would have been activated for a while to become self aware, It also may have had access to the NET to learn about human's, To create the virus, Skynet would have needed the ability to program.
Earlier in the film The cell phone network goes's down, The terminator is also heard, "Skynet is taking over GLOBAL communication, in preparation for its attack".
The virus would have been created by skynet as a decoy, so that skynet could get control of the USA's government, The missile code's etc.

At some point in time, between the time line of T2 and T3 "skynet" the computer and programme's would have been made/developed, skynet would have been operational before going "online" onto the defense network, Skynet needed the defense network in order to gain access to the missile codes and location's.

The US military completed it at the same time in those timelines too by using Cyberdyne's backup files stored off site... but for some reason weren't idiot enough to give it control of everything straight away. Its first few years of life were dominated by mankind, so that should have affected its disposition

Originally posted by shaber The US military completed it at the same time in those timelines too by using Cyberdyne's backup files stored off site

Where do you figure this part from? I'm not familiar with any Terminator literature so if the above is stated in any comics/books then please forgive me...But where is there evidence of "Cyberdyne's backup files" in the movies? Thanks in advance.